Recombinant microorganisms for increased production of organic acids

Title: Recombinant microorganisms for increased production of organic acids.Abstract: Disclosed are recombinant microorganisms for producing organic acids. The recombinant microorganisms express a polypeptide that has the enzymatic activity of an enzyme that is utilized in the pentose phosphate cycle. The recombinant microorganism may include recombinant Actinobacillus succinogenes that has been transformed to express a Zwischenferment (Zwf) gene. The recombinant microorganisms may be useful in fermentation processes for producing organic acids such as succinic acid and lactic acid. Also disclosed are novel plasmids that are useful for transforming microorganisms to produce recombinant microorganisms that express enzymes such as Zwf. ...

This application claims the benefit under 35 U.S.C. § 119(e) of U.S. provisional application No. 60/647,141, filed on Jan. 26, 2005; and U.S. provisional application No. 60/639,443, filed on Dec. 22, 2004. The aforementioned applications are incorporated herein by reference in their entireties.

STATEMENT REGARDING U.S. GOVERNMENT SUPPORT

This invention was made with support from the United States Government under Cooperative Agreement No. DE-FC36-02GO12001 awarded by the Department of Energy. The United States Government has certain rights in this invention.

BACKGROUND

Many chemicals that are currently derived from petrochemical materials could be produced from naturally occurring carbohydrates. In particular, succinic acid, a four-carbon dicarboxylic acid, has the potential to become a high volume commodity chemical that could be used as starting material for commercial processes that produce many important intermediate and specialty chemicals for the consumer product industries and that currently rely on starting materials derived from non-renewable petrochemical materials. For example, as a commodity chemical, succinic acid could replace petrochemical starting materials used in the production of 1,4-butanediol (BDO) and tetrahydrofuran (THF) compounds, which are useful as solvents and starting materials for many industries. For example, BDO and THF compounds are useful for producing resins for automotive bodies, thermoplastics for use in household appliances, and elastic polymers such as Lycra™ in the textile industry. In addition, BDO and THF compounds also have many specialty uses in the agrochemical and pharmaceutical industries. Notably, worldwide consumption of BDO is expected to increase at an annual rate as high as 4%.

The petrochemicals currently used to produce BDO and THF include acetylene, formaldehyde, butane, butadiene, and propylene oxide. All of these have various hazardous properties, such as extreme flammability, chemical instability and toxicity. Further, as these materials are derived from petroleum, they deplete a non-renewable resource, and upon disposal or destruction, ultimately release carbon (as carbon dioxide) into the atmosphere. Thus, developing succinic acid as a replacement for petrochemically derived materials would reduce handling and storage of hazardous materials, enhance industrial and community safety, reduce pollution and environmental costs, and reduce dependence on oil.

Production of succinic acid and other organic compounds by fermentation of sugars is economically feasible. A number of microorganisms have been used to produce succinic acid using corn sugars as a carbon source. As such, developing succinic acid as replacement for petrochemical starting materials would expand markets for corn, and other agricultural products and/or biomass that can provide fermentable sugars.

Formally, the biochemical pathway for succinic acid production adds a carbon dioxide molecule to the three carbon compound phosphoenolpyruvate (PEP), to produce the four carbon compound oxaloacetate (OAA). The next steps in the pathway to succinic acid are part of the reverse tricarboxylic acid cycle (TCA cycle) and include two obligate reduction steps. In the biochemical process leading from OAA to succinate, OAA must first be reduced to produce L-malate. L-malate is then dehydrated to produce fumarate and water. Fumarate is then reduced to give the succinic acid. In the chemical arts, “reduction” refers to the addition of molecular hydrogen to a compound.

Generally, free molecular hydrogen is not found in intracellular biological systems. Rather, reduction is performed through the use of coenzymes that function as biochemical equivalents of hydrogen (i.e., as carriers of molecular hydrogen) and are termed “reducing equivalents.” Reducing equivalents include the coenzymes nicotinamide adenine dinucleotide hydrogen (“NADH”), nicotinamide adenine dinucleotide phosphate hydrogen (“NADPH”), flavine adenine dinucleotide hydrogen (“FADH2”), and flavin mononucleotide hydrogen (“FMNH”). Generally, NADH and NADPH may be interconverted in a range of microorganisms by the enzyme pyridine dinucleotide transhydrogenase.

The reducing equivalents required to transform OAA to succinate are provided by NAD(P)H2, FADH2, or other co-factors. It is essential that a sufficient quantity of reducing equivalents is available for the transformation of OAA to succinate. If sufficient reducing equivalents are not available, the biochemical pathway will not function efficiently, and only a portion of the OAA will be transformed into the desired succinate.

Reducing equivalents may be produced in a number of biological processes that are commonly found in cellular metabolism. For example, reducing equivalents may be generated in the pentose phosphate cycle (PPC). In the PPC, glucose-6-phosphate is converted to D-6-phospho-glucono-δ-lactone by the enzyme glucose-6-phosphate dehydrogenase, which is also known as Zwischenferment enzyme or Zwf. As part of this conversion, NADP is converted to NADPH as an acceptor of reducing equivalents.

Few microorganisms have been described which produce sufficient concentrations of succinic acid for commercial production. One such microorganism is Actinobacillus succinogenes, a facultative anaerobe that was isolated from the bovine rumen. This organism produces high concentration of succinic acid and tolerates high sugar concentration. Actinobacillus succinogenes is one of the best known producers of succinic acid, but the fermentative yields of this strain may be limited by the lack of reducing equivalents. As such, improvements are desirable to increase the yield of succinic acid produced by fermentation, including the use of improved strains of microorganisms for producing succinic acid.

SUMMARY

Disclosed are recombinant microorganisms for producing organic acids. The recombinant microorganisms expresses a polypeptide that has one or more biochemical activities of an enzyme utilized in the pentose phosphate cycle. In one embodiment, the enzyme is glucose-6-phosphate-1-dehydrogenase, also called Zwischenferment enzyme or Zwf. For example, the recombinant microorganism may express a polynucleotide that encodes a polypeptide having Zwf enzyme activity. In one embodiment, the recombinant microorganism is a recombinant strain of a succinic acid producing microorganism which has been transformed with a DNA molecule that expresses a polypeptide having Zwf enzyme activity.

The recombinant microorganism typically is capable of producing one or more organic acids at a level suitable for commercial production. In some embodiments, the recombinant microorganism is a succinic acid producing microorganism. For example, the microorganism may produce succinic acid at a concentration suitable for commercial production. A concentration suitable for commercial production may be at least about 20 g/L, 40 g/L, 60 g/L, 80 g/L, 100 g/L, 120 g/L, and/or 140 g/L. Desirably, the recombinant microorganism is capable of producing succinic acid at concentrations of about 50 g/L to about 130 g/L.

The recombinant microorganism may be selected and/or recombinantly engineered to tolerate relatively high concentrations of succinic acid to facilitate production of succinic acid at a concentration suitable for commercial production in a fermentation system. In some embodiments, the recombinant microorganism may be selected to produce relatively low amounts of undesirable by-products such as acetate, formate, and/or pyruvate (e.g., no more than about 2.0 g/L acetate, no more than about 2.0 g/L formate, and/or no more than about 3.0 g/L pyruvate). The recombinant microorganism may be derived from a strain (or a variant of a strain) that is resistant to levels of sodium monofluoroacetate at concentration of at least about 1 g/L, 2 g/L, 4 g/L, and/or 8 g/L. In another embodiment, a variant of the recombinant microorganism may be selected to be resistant to levels of sodium monofluoroacetate at concentration of at least about 1 g/L, 2 g/L, 4 g/L, and/or 8 g/L.

In one embodiment, the recombinant microorganism is derived from a strain of Actinobacillus succinogenes (i.e., “A. succinogenes”) or a microorganism related to Actinobacillus succinogenes. One suitable strain of A. succinogenes is Bacterium 130Z deposited with the American Type Culture Collection (ATCC), under ATCC Accession Number 55618. See U.S. Pat. No. 5,504,004 for description of Bacterium 130Z and other suitable strains.

Other suitable microorganisms may be selected for preparing the recombinant microorganism and may include microorganisms which are related to A. succinogenes as determined by sequence identity within 16S rRNA. For example, a suitable microorganism related to A. succinogenes may have 16S rRNA that exhibits substantial sequence identity to A. succinogenes 16S rRNA (i.e., a microorganism having 16S rRNA that exhibits at least about 90% sequence identity to A. succinogenes 16S rRNA or more suitably, that exhibits at least about 95% sequence identity to A. succinogenes 16S rRNA). Many representative microorganisms of the family Pasteurellaceae have 16S rRNA that exhibits at least about 90% sequence identity to A. succinogenes 16S rRNA. For example, see Guettler et al., INT'L J. SYSTEMATIC BACT. (1999), 49, 207-216 at page 209, Table 2. Suitable microorganisms may include microorganisms such as Bisgaard Taxon 6 and Bisgaard Taxon 10.

In some embodiments, the recombinant microorganism may be prepared from organisms other than A. succinogenes. For example, the recombinant microorganism may be prepared from any microorganism that is suitable for use in fermentation systems for producing organic acids. A suitable microorganism may include E. coli. Suitable strains of E. coli are known in the art.

Variants of microorganisms that are resistant to sodium monofluoroacetate may also be suitable for preparing the recombinant microorganism. For example, see U.S. Pat. No. 5,521,075 and U.S. Pat. No. 5,573,931. In one embodiment, the recombinant microorganism is prepared from a variant of A. succinogenes that is resistant to at least about 1 g/L sodium monofluoroacetate. One suitable variant is FZ45. See U.S. Pat. No. 5,573,931. The recombinant microorganism deposited under ATCC Accession Number PTA-6255, is derived from a variant of A. succinogenes that is resistant to at least about 1 g/L sodium monofluoroacetate (i.e., FZ45).

The recombinant microorganism typically is transformed with a polynucleotide encoding a polypeptide that has one or more biochemical activities of an enzyme utilized in the pentose phosphate cycle. For example, the recombinant microorganism may be transformed with a polynucleotide that encodes a polypeptide having one or more biochemical activities of the Zwf enzyme (i.e., glucose-6-phosphate dehydrogenase activity and/or NADP reductase activity). Desirably, the polynucleotide encodes a polypeptide that facilitates the conversion of NADP to NADPH. The polynucleotide or polypeptide may be endogenous to the microorganism or derived from a gene or enzyme normally present in the microorganism. In some embodiments, the polynucleotide or polypeptide may be homologous to an endogenous gene or enzyme of the microorganism. In other embodiments, the polynucleotide or polypeptide may be heterologous (i.e., derived from a gene or enzyme normally not present in the microorganism or derived from a source other than the microorganism).

The recombinant microorganism may express a variant of the polynucleotide that encodes the polypeptide and/or a variant of the polypeptide. A variant of the polynucleotide may include a polynucleotide having at least about 90% sequence identity to the polynucleotide, or desirably, at least about 95% sequence identity to the polynucleotide, where the polynucleotide encodes a polypeptide that has one or more biochemical activities of the Zwf enzyme (e.g., NADP reductase activity). A variant may include a polypeptide that has at least about 90% sequence identity to the polypeptide, or desirably, at least about 95% sequence identity to the polypeptide, where the polypeptide has one or more biochemical activities of the Zwf enzyme (e.g., NADP reductase activity). As such, suitable polynucleotides may include polynucleotides encoding a polypeptide having at least about 95% sequence identity to a selected Zwf enzyme, where the polypeptide has NADP reductase activity.

The recombinant microorganism may be transformed with a polynucleotide that expresses a polypeptide having Zwf enzyme activity, where the recombinant microorganism exhibits higher Zwf enzyme activity than a microorganism which has not been transformed with a polynucleotide that expresses a polypeptide having Zwf enzyme activity. In some embodiments, the recombinant microorganism exhibits at least about five times (5×) more Zwf enzyme activity, (or desirably at least about ten times (10×) more Zwf enzyme activity, or more desirably at least about fifty times (50×) more Zwf enzyme activity), than a microorganism which has not been transformed with a polynucleotide that expresses a polypeptide having Zwf enzyme activity. Zwf enzyme activity may include NADP reductase activity. Zwf enzyme activity may be determined by measuring the level of NADPH present the recombinant microorganism (e.g., as compared to a microorganism which has not been transformed with a polynucleotide that expresses a polypeptide having Zwf enzyme activity).

The recombinant microorganism may express a polynucleotide that encodes a Zwf enzyme such as a Zwf gene. A variant of the polynucleotide may comprise a polynucleotide having at least about 90% sequence identity to a Zwf gene, or desirably, at least about 95% sequence identity to a Zwf gene and encoding a polypeptide that has one or more biochemical activities of the Zwf enzyme. A variant of a polynucleotide may include a nucleic acid fragment of the polynucleotide. For example, a fragment may include at least about 90% of a Zwf gene, or at least about 95% of a Zwf gene. A nucleic acid fragment may be any suitable length. For example, the nucleic acid fragment may comprise at least about 10, 50, 100, 250, 500, 1000 and/or 1400 nucleotides. A fragment may encode a polypeptide that has one or more biochemical activities of the Zwf enzyme.

Suitable Zwf genes may include Zwf genes endogenous or native to the recombinant microorganism (i.e., Zwf genes normally present in the microorganism from which the recombinant microorganism is derived), or variants thereof. Other suitable Zwf genes may include Zwf genes heterologous to the microorganism (i.e., Zwf genes normally not present in, or obtained from sources other than the microorganism used to prepare the recombinant microorganism), or variants thereof. Suitable Zwf genes may include variants that have at least about 90% sequence identity to the polynucleotide sequence of the selected Zwf gene (preferably at least about 95% sequence identity to the polynucleotide sequence of the selected Zwf gene) and that encode a polypeptide that has one or more biochemical activities of the Zwf enzyme (i.e., glucose-6-phosphate dehydrogenase activity and/or NADP reductase activity).

Suitable Zwf genes may include the E. coli Zwf gene or variants thereof. The polynucleotide sequence of the E. coli Zwf gene is deposited with GenBank under accession number NC—000913, reverse complement of nucleotides 1,932,863 to 1,934,338 (SEQ ID NO:1) and under accession number M55005, nucleotides 708 to 2180 (SEQ ID NO:2). Suitable variants of the E. coli Zwf gene may include a polynucleotide having at least about 90% sequence identity (desirably at least about 95% sequence identity) to the polynucleotide of SEQ ID NO:1 (or SEQ ID NO:2), such that the polynucleotide encodes a polypeptide that has one or more biochemical activities of the Zwf enzyme (i.e., glucose-6-phosphate dehydrogenase activity and/or NADP reductase activity).

Suitable Zwf genes may include the A. succinogenes Zwf gene or variants thereof. The draft genome sequence for A. succinogenes 130Z has recently been established and assembled and is publicly available as of September 2005, at the Joint Genome Institute, Department of Energy website. The Zwf gene is annotated as “glucose-6-phosphate 1-dehydrogenase” and is present on contig 115, nucleotides 8738-10225 (i.e., SEQ ID NO:5). The predicted amino acid sequence of encoded polypeptide (i.e., the A. succinogenes Zwf enzyme) is presented as SEQ ID NO:6. The Zwf enzyme exhibits 43% amino acid sequence identity and 60% amino acide homology to the E. coli Zwf enzyme using the “BLAST” alignment algorithm version BLASTP 2.2.12, BLOSUM62 matrix, available at the National Center for Biotechnology Information website. Suitable variants of the A. succinogenes Zwf gene may include a polynucleotide having at least about 90% sequence identity (desirably at least about 95% sequence identity) to the polynucleotide of SEQ ID NO:5, such that the polynucleotide encodes a polypeptide that has one or more biochemical activities of the Zwf enzyme (i.e., glucose-6-phosphate dehydrogenase activity and/or NADP reductase activity).

The recombinant microorganism may express an endogenous Zwf enzyme (i.e., a Zwf enzyme present within the microorganism from which the recombinant microorganism is derived), or variants thereof. In other embodiments, the recombinant microorganism may express a Zwf enzyme that is heterologous to the microorganism (i.e., a Zwf enzyme that is not present or expressed in the microorganism from which the recombinant microorganism is derived), or variants thereof. Suitable Zwf enzymes may include variants having at least about 90% amino acid sequence identity to the amino acid sequence of a selected Zwf enzyme (desirably at least about 95% amino acid sequence identity to the selected Zwf enzyme) and having one or more biochemical activities of the Zwf enzyme (e.g., NADP reductase activity and/or glucose-6-phosphate dehydrogenase activity). Suitable Zwf enzymes may include the E. coli Zwf enzyme (e.g., SEQ ID NO:3, polypeptide encoded by the reverse complement of the nucleotide sequence of nucleotides 1,932,863 to 1,934,338 of NC—000913) or variants thereof, and the A. succinogenes Zwf enzyme (e.g., SEQ ID NO:6) or variants thereof.

A variant polypeptide may include a fragment of a Zwf enzyme. For example, a fragment may include at least about 90% of the amino acid sequence of SEQ ID NO:3, or more desirably at least about 95% of the amino acid sequence of SEQ ID NO:3. In other embodiments, a fragment may include at least about 90% of the amino acid sequence of SEQ ID NO:6, or more desirably at least about 95% of the amino acid sequence of SEQ ID NO:6. A polypeptide fragment may be any suitable length. For example, the polypeptide fragment may comprise at least about 10, 50, 100, 200, and/or 300 amino acids (e.g., of SEQ ID NO:3 or SEQ ID NO:6). A polypeptide fragment typically has one or more biochemical activities of the Zwf enzyme.

The recombinant microorganism may include a succinic acid producing microorganism that has been transformed with a polynucleotide that expresses an endogenous (i.e., native) Zwf gene which encodes an endogenous (i.e., native) Zwf enzyme. In some embodiments, the recombinant microorganism may include a succinic acid producing microorganism that has been transformed with a polynucleotide that expresses a heterologous Zwf gene which encodes a heterologous Zwf enzyme. The recombinant microorganism deposited with the American Type Culture Collection (ATCC), under ATCC Accession Number PTA-6255, is a recombinant strain of a succinic acid producing microorganism (i.e., A. succinogenes) that expresses a heterologous Zwf gene (e.g., the E. coli Zwf gene) which encodes a heterologous Zwf enzyme.

The recombinant microorganism may express a polypeptide having Zwf enzyme activity at relatively high levels (i.e., the polypeptide may be “overexpressed”). For example, the recombinant microorganism may express an endogenous Zwf enzyme at relatively high levels as compared to a non-recombinant microorganism. In some embodiments, the recombinant microorganism may be transformed with a DNA molecule (e.g., a plasmid) that expresses an endogenous Zwf enzyme at relatively high levels compared to a recombinant microorganism that has not been transformed with the DNA molecule.

A polynucleotide, such as a Zwf gene, may be optimized for expression in a selected microorganism from which the recombinant microorganism is derived. For example, a heterologous Zwf gene may be optimized for expression in a non-native microorganism. In some embodiments, a Zwf gene may be optimized for expression in A. succinogenes, or in a microorganism such as Bisgaard Taxon 6 or Bisgaard Taxon 10. In other embodiments, a Zwf gene may be optimized for expression in E. coli.

A polynucleotide such as a Zwf gene may be optimized for expression in the recombinant microorganism by any suitable strategy. For example, a Zwf gene may be optimized for expression in the recombinant microorganism by operably linking the Zwf gene to a promoter sequence that facilitates expression of the Zwf gene in the recombinant microorganism. The promoter sequence may be optimized to facilitate relatively high levels of expression in the recombinant microorganism (i.e., optimized to facilitate “overexpression”). The Zwf gene may be operably linked to a promoter sequence that is endogenous to the microorganism (i.e., a promoter native to the microorganism) or heterologous to the microorganism (i.e., a promoter normally not present in, or derived from a source other than the microorganism). Suitable promoters may include promoters that are not the native promoter for the selected Zwf gene (i.e., a non-Zwf gene promoter, which may be endogenous to the microorganism or heterologous to the microorganism). Suitable promoters may include inducible promoters or constitutive promoters. Suitable promoters may be derived from promoters of succinic acid producing microorganisms.

In other embodiments, expression of a Zwf gene may be optimized at the translational level. For example, a heterologous Zwf gene may be modified to include codons that demonstrate preferred usage frequency in the microorganism from which the recombinant microorganism is derived as a non-natural host for the gene.

In another embodiment, expression of a polynucleotide such as a Zwf gene may be optimized by providing a relatively high copy number of the polynucleotide in the recombinant microorganism. For example, a Zwf gene may be present on an epigenetic element that is capable of replicating to achieve a relatively high copy number in the recombinant microorganism (e.g., a plasmid).

In some embodiments, the recombinant microorganism is a recombinant strain of a succinic acid producing microorganism, such as Actinobacillus succinogenes or related microorganisms, which has been transformed with a DNA molecule that includes a promoter operationally linked to a Zwf gene. The Zwf gene may be derived from an endogenous or heterologous Zwf gene and may include, for example, the A. succinogenes Zwf gene (e.g., SEQ ID NO:5) and the E. coli Zwf gene (e.g., SEQ ID NOs: 1 & 2). Other Zwf genes are known and their polynucleotide sequences have been published (See, e.g., GenBank). Suitable endogenous or native promoter sequences of succinic acid producing microorganisms may include, for example, the phosphoenolpyruvate (PEP) carboxykinase promoter sequence. The A. succinogenes phosphoenolpyruvate (PEP) carboxykinase promoter sequence is deposited with GenBank under accession number AY308832, nucleotides 1-258 (SEQ ID NO:4). A phosphoenolpyruvate (PEP) carboxykinase promoter may be a suitable heterologous promoter for a Zwf gene (i.e., a non-Zwf gene promoter).

As described herein, a recombinant microorganism may include a recombinant DNA molecule as an epigenetic element and/or the recombinant DNA molecule may be incorporated into the genome of the microorganism (e.g., by appropriate methods of recombination). In certain embodiments, the DNA molecule is a plasmid, a recombinant bacteriophage, a bacterial artificial chromosome (3AC) and/or an E. coli P1 artificial chromosome (PAC). The DNA molecule may include a selectable marker. Suitable selectable markers may include markers for kanamycin resistance, ampicillin resistance, tetracycline resistance, chloramphenicol resistance, and combinations of these selectable markers. In one embodiment, the selectable marker is kanamycin resistance.

As described herein, a recombinant DNA molecule may include a suitable promoter operationally linked to a polynucleotide that encodes a polypeptide having one or more biochemical activities of Zwf enzyme for expressing the polynucleotide in a recombinant microorganism (e.g., A. succinogenes). The promoter may be suitable for expressing the polypeptide in a succinic acid producing microorganism. In some embodiments, the recombinant DNA molecule includes a phosphoenol pyruvate (PEP) carboxykinase promoter (e.g., a A. succinogenes phosphoenol pyruvate (PEP) carboxykinase promoter) operationally linked to a Zwf gene or a variant thereof, (which may include a heterologous Zwf gene such as an E. coli Zwf gene or an A. succinogenes Zwf gene). For example, the DNA molecule may include nucleotides 1-258 of the DNA sequence deposited under GenBank accession number AY308832 (SEQ ID NO:4) or a variant thereof, operationally linked to the reverse complement of nucleotides 1,932,863 to 1,934,338 of the DNA sequence deposited under GenBank accession number NC—000913 (SEQ ID NO:1); or operationally linked to the DNA sequence deposited under GenBank accession number M55005 (SEQ ID NO:2); or operationally linked to the DNA sequence of SEQ ID NO:5. In some embodiments, the promoter may include a polynucleotide having at least about 95% sequence identity to the polynucleotide of SEQ ID NO:4 and having promoter activity in the recombinant microorganism.

A recombinant microorganism comprising the recombinant DNA molecule may be suitable for producing an organic acid (e.g., succinic acid or lactic acid) in a fermentation system. The recombinant microorganism comprising the recombinant DNA molecule may produce enhanced levels of an organic acid (e.g., succinic acid or lactic acid) in a fermentation system relative to a microorganism that does not comprise the recombinant DNA molecule.

Also disclosed is a DNA plasmid comprising one or more of the aforementioned recombinant DNA molecules. The DNA plasmid may include a selectable marker. Suitable selectable markers may include one or more of the genes for ampicillin resistance, streptomycin resistance, kanamycin resistance, tetracycline resistance, chloramphenicol resistance, and sulfonamide resistance, operationally linked to a suitable promoter (e.g., a constitutive promoter). In one embodiment, the DNA plasmid includes the gene for kanamycin resistance.

The DNA plasmid may include sequences required for maintaining and/or replicating the plasmid in one or more suitable host cells. In one embodiment, the DNA plasmid is capable of functioning as a shuttle vector between suitable host cells. The DNA plasmid may be capable of functioning as a shuttle vector between A. succinogenes and E. coli.

Also disclosed is a host cell that includes one or more of the aforementioned DNA molecules. For example, the host cell may comprise a DNA plasmid that includes the DNA molecule. The host cell may be suitable for producing and isolating a DNA plasmid that includes the DNA molecule.

The host cell may be suitable for producing one or more organic acids in a fermentation system. In some embodiments, the host cell expresses a Zwf gene (and subsequently a Zwf enzyme) at a level suitable for enhancing the production or one or more organic acids (e.g., succinic acid or lactic acid) in a fermentation system. In some embodiments, the host cell may expresses a Zwf gene (and subsequently a Zwf enzyme) at a level suitable for enhancing the concentration of reducing equivalents (e.g., NADPH) in the host cell. The host cell may comprise a recombinant strain of A. succinogenes that expresses a Zwf gene (and subsequently a Zwf enzyme) at a level suitable for enhancing the concentration of reducing equivalents (e.g., NADPH) in the strain. Such a strain may be suitable for producing enhanced levels of succinic acid in a fermentation system relative to a strain that does not comprise the recombinant DNA molecule.

In some embodiments, the host cell is capable of producing succinic acid at concentrations of at least about 20 g/L, 40 g/L, 60 g/L, 80 g/L, 100 g/L, 120 g/L, 140 g/L, and/or 160 g/L (e.g., in a fermentation system). In certain embodiments, the host cell is capable of producing succinic acid at concentrations of at about 50 g/L to about 130 g/L. Desirably, the host cell does not produce selected organic acids other than succinic acid at substantial concentrations. Where the host cell produces organic acids other than succinic acid (e.g., acetic acid, formic acid, pyruvic acid, and mixtures thereof), desirably the organic acids other than succinic acid are produced at concentrations no more than about 30 g/L, more desirably no more than about 20 g/L, more desirably no more than about 10 g/L, and even more desirably no more than about 5 g/L.

The aforementioned recombinant microorganisms may be used in methods that include fermenting a nutrient medium to produce one or more organic acids. In some embodiments, the methods may include fermenting a nutrient medium with a recombinant microorganism that expresses a Zwf gene (e.g., the E. coli Zwf gene). Organic acids produced by the method may include succinic acid and lactic acid. In further embodiments, the methods are suitable for producing succinic acid at concentrations of at least about 20 g/L, 40 g/L, 60 g/L, 80 g/L, 100 g/L, 120 g/L, and/or 160 g/L.

In particular, the methods may include fermenting a nutrient medium with a recombinant strain of A. succinogenes that expresses a Zwf gene (and subsequently a Zwf enzyme) at a level suitable for enhancing the production of an organic acid (e.g., succinic acid). The Zwf gene may include a heterologous Zwf gene. A recombinant strain of A. succinogenes that expresses a heterologous Zwf gene (i.e., the E. coli Zwf gene) is deposited under ATCC accession number PTA-6255. In certain embodiments, the recombinant microorganism is a recombinant strain of a microorganism such as Bisgaard Taxon 6 or Bisgaard Taxon 10 that expresses a Zwf gene (which may be heterologous) at a level suitable for enhancing the production of an organic acid (e.g., succinic acid). Suitable recombinant microorganisms also include recombinant strains of E. coli that express a Zwf gene (which may be heterologous) at a level suitable for enhancing the production of an organic acid (e.g., lactic acid).

In the method, it may be desirable to ferment a nutrient medium with recombinant microorganisms that produce relatively high levels of selected organic acids, such as succinic acid and/or lactic acid. As such, the selected recombinant microorganisms may be resistant to high levels of organic acids, such as succinic and/or lactic acid. The recombinant microorganisms may also be selected to produce relatively low levels of other undesirable by-products. For example, the recombinant microorganism may produce relatively low levels of acetate, formate, pyruvate, and mixtures thereof (e.g., no more than about 2.0 g/L, no more than about 2.0 g/L formate, and/or no more than about 3.0 g/L pyruvate). The above-described recombinant microorganisms that are resistant to concentrations of sodium monofluoroacetate of about 1 g/L, 2 g/L, 4 g/L, and/or 8 g/L are suitable for the method.

In the method, the nutrient medium typically includes a fermentable carbon source. A fermentable carbon source may be provided by a fermentable biomass. In one embodiment, the fermentable carbon source is derived from feedstock, including sugar crops, starch crops, and/or cellulosic crop residues. Generally, the fermentable carbon source is a sugar, such as glucose. The fermentable carbon source may also include sugar alcohols. In suitable embodiments, the method results in a succinic acid yield (g) of at least about 100% relative to glucose (g).

FIG. 3: Zwf enzymatic activities in cell extracts of transformed strains. Extracts were prepared and assayed for Zwf activity as described below. All strains carrying pJR762.73 showed orders of magnitude increases in Zwf activity, which is graphed on a logarithmic scale.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

Disclosed herein is a recombinant microorganism which expresses a polypeptide that has one or more biochemical activities of an enzyme utilized in the pentose phosphate cycle. As used herein, “microorganism” includes any suitable single-cell organism such as bacteria, fungi, and yeast. As used herein, “recombinant microorganism” means a microorganism that has been modified in a manner that results in a non-naturally occurring microorganism. A “recombinant microorganism” may include a microorganism that has been transformed with a DNA molecule (e.g., a recombinant DNA molecule).

A recombinant microorganism may include a microorganism that has been transformed with a DNA molecule that expresses a polypeptide having one or more biochemical activities of the Zwf enzyme. The pentose phosphate cycle utilizes several enzymes including glucose-6-phosphate-1-dehydrogenase, (also called Zwischenferment enzyme or Zwf); 6-phosphogluconolactonase; 6-phosphogluconate dehydrogenase, (also called Gnd); ribose-5-phosphate isomerase A and B; ribulose phosphate 3-epimerase; transketolase I and II; and transaldolase A and B. Of these enzymes, Zwf and Gnd result in the production of two hydrogen equivalents in the form of NADPH.

The recombinant microorganism may express any suitable polypeptide or variant thereof having one or more biochemical activities of the Zwf enzyme (e.g., glucose-6-phosphate-1-dehydrogenase activity and NADP reductase activity). For example, one suitable Zwf enzyme is the E. coli Zwf enzyme or a variant thereof. In some embodiments, the recombinant microorganism may express the Zwf enzyme at elevated levels (i.e., “overexpress” the enzyme) relative to levels present in non-recombinant microorganisms.

The recombinant microorganism may express a variant polypeptide having at least about 90% sequence identity to the amino acid sequence of a Zwf enzyme, and more desirably at least about 95% sequence identity to the amino acid sequence of a Zwf enzyme. In suitable embodiments, the recombinant microorganism may express a variant of a Zwf enzyme that has at least about 96%, 97%, 98%, or 99% sequence identity to the Zwf enzyme. Desirably, the variant polypeptide has one or more biochemical activities of the Zwf enzyme. A variant polypeptide may include a fragment of the Zwf enzyme. Suitable Zwf enzymes include A. succinogenes Zwf enzyme, E. coli Zwf enzyme, and variants thereof.

The recombinant microorganism may express a polynucleotide encoding a polypeptide having one or more biochemical activities of the Zwf enzyme such as a Zwf gene or a variant thereof. For example, the recombinant microorganism may express a Zwf gene or a variant comprising a DNA sequence that has at least about 90% sequence identity to the Zwf gene, and more desirably at least about 95% sequence identity to the Zwf gene. In suitable embodiments, the recombinant microorganism may express a variant of the Zwf gene comprising a DNA sequence that has at least about 96%, 97%, 98%, or 99% sequence identity to the Zwf gene. Desirably, the variant polynucleotide encodes a polypeptide having one or more biochemical activities of Zwf enzyme. A variant polynucleotide may include a fragment of the Zwf gene. In some embodiments, the recombinant microorganism may express an A. succinogenes Zwf gene, an E. coli Zwf gene, or a variant thereof.

The recombinant microorganism may be derived from any suitable microorganism. Typically, the microorganism is capable of producing an organic acid at a level suitable for commercial production. As used herein, an “organic acid” includes at least one carboxylic group. For example, “organic acid” includes succinic acid and lactic acid. As used herein, organic acids may be alternately designated by the organic acid anion or a salt thereof. For example, “succinic acid” may be referred to as “succinate”; “lactic acid” may be referred to as “lactate”; “formic acid” may be referred to as “formate”; and “pyruvic acid” may be referred to as “pyruvate.”

The recombinant microorganism typically expresses a Zwf gene, which may be a heterologous Zwf gene. The Zwf gene may be optimized for expression in the recombinant microorganism. For example, the Zwf gene may be operationally linked to a promoter that facilitates overexpression of the gene in the recombinant microorganism relative to a non-recombinant microorganism. The promoter may be endogenous to the microorganism (i.e., native to the microorganism from which the recombinant microorganism is derived) or heterologous to the microorganism (i.e., not native to the microorganism from which the recombinant microorganism is derived or obtained from a source other than the microorganism). The promoter may be endogenous to the Zwf gene or heterologous to the Zwf gene (i.e., a non-Zwf gene promoter). The promoter may facilitate constitutive and/or inducible expression of the Zwf gene, and/or the promoter may be modified to facilitate constitutive and/or inducible expression of the Zwf gene by suitable methods.

The Zwf gene may be modified to facilitate translation of the corresponding mRNA. For example, the Zwf gene may be modified to include codons that are not present in the endogenous or native gene. These non-endogenous codons may be selected to reflect the codon usage frequency in the recombinant microorganism. Codon usage tables have been developed for many microorganisms and are known in the art. The Zwf gene may be modified to reflect the codon usage frequency for A. succinogenes as provided below:

The recombinant microorganism may include a recombinant strain of A. succinogenes that expresses a Zwf gene (e.g., an endogenous Zwf gene and/or a heterologous Zwf gene such as the E. coli Zwf gene). Other suitable microorganisms for producing recombinant microorganisms include Bisgaard Taxon 6 (deposited with the Culture Collection, University of Göteborg, Sweden (CCUG), under accession number 15568); Bisgaard Taxon 10 (deposited under CCUG accession number 15572); and any suitable strain of E. coli for which many strains are known in the art. The recombinant microorganism may be derived from a strain that produces high levels of one or more organic acids such as succinic acid and lactic acid, and/or the recombinant microorganism may be selected and/or engineered to produce high or enhanced levels of one or more organic acids such as succinic acid and lactic acid relative to a non-recombinant microorganism.

The recombinant microorganism may be derived from strains that are resistant to relatively high levels of undesirable by-products and/or strains of microorganisms that produce relatively low levels of undesirable by-products. Undesirable by-products may include formate (or formic acid), acetate (or acetic acid), and/or pyruvate (or pyruvic acid). Methods for selecting strains that produce low levels of acetate are known in the art. See, e.g., U.S. Pat. No. 5,521,075 and U.S. Pat. No. 5,573,931, which are incorporated herein by reference. For example, strains of microorganisms that produce relatively low levels of acetate may be selected by growing the microorganisms in the presence of a toxic acetate derivative, such as sodium monofluoroacetate at a concentration of about 1.0 to about 8.0 g/L. Selected strains may produce relatively low levels of acetate (e.g., less than about 2.0 g/L), formate (e.g., less than about 2.0 g/L), and/or pyruvate (e.g., less than about 3.0 g/L) in a glucose fermentation. One suitable monofluoroacetate resistant strain for producing a recombinant microorganism is a strain of A. succinogenes called FZ45, which is a derivative of A. succinogenes deposited under ATCC accession number 55618. See U.S. Pat. No. 5,573,931, which describes suitable methods for preparing microbial strains that are resistant to monofluoroacetate.

The recombinant microorganism may be selected and/or engineered to be resistant to relatively high levels of undesirable by-products and/or to produce relatively low levels of undesirable by-products. For example, after transformation, a population of recombinant microorganisms may be grown in the presence of sodium monofluoroacetate to select strains that are resistant to relatively high levels of acetate and/or strains that produce relatively low levels of acetate.

A DNA sequence that encodes a polypeptide with one or more biochemical activities of the Zwf enzyme may be obtained by employing methods known in the art (e.g., PCR amplification of a Zwf gene with suitable primers and cloning into a suitable DNA vector). The polynucleotide sequences of suitable Zwf genes have been disclosed. (See, e.g., GenBank). For example, the polynucleotide sequence of the A. succinogenes Zwf gene has been published (SEQ ID NO:5 & 6). (See Joint Genome Institute, Department of Energy website). The E. coli Zwf gene is deposited with GenBank (e.g., under GenBank Accession Number NC—000913 (SEQ ID NO:1) and GenBank Accession Number M55005 (SEQ ID NO:2)). The Zwf gene or variants thereof may be obtained by PCR amplification of a microorganism's genomic DNA with appropriate primers.

The DNA vector may be any suitable vector for expressing the gene in a recombinant microorganism. Suitable vectors include plasmids, artificial chromosomes (e.g., bacterial artificial chromosomes), and/or modified bacteriophages (e.g., phagemids). The vector may be designed to exist as an epigenetic element and/or the vector may be designed to recombine with the genome of the microorganism.

The DNA molecule typically includes a promoter operationally linked to a polynucleotide that encodes a polypeptide having Zwf enzyme activity. The promoter may be endogenous or native to the microorganism from which the recombinant microorganism is derived, or heterologous to the microorganism (i.e., derived from a source other than the recombinant microorganism). Furthermore, the promoter may be the native promoter for a selected Zwf gene or may be a promoter other than the native promoter for a selected Zwf gene (i.e., a non-Zwf gene promoter). Where the recombinant microorganism is a strain of A. succinogenes, a suitable endogenous or native promoter is the A. succinogenes phosphoenolpyruvate (PEP) carboxykinase promoter (SEQ ID NO:4), deposited under GenBank accession number AY308832, including nucleotides 1-258, or a variant thereof. The promoter may be operationally linked to the Zwf gene using cloning methods that are known in the art. For example, the promoter and Zwf gene may be amplified by PCR using primers that include compatible restriction enzyme recognition sites. The amplified promoter and gene then may be digested with the enzyme and cloned into an appropriate vector that includes a suitable multiple cloning site.

In addition, the DNA molecule may include a selectable marker. The selectable marker may impart resistance to one or more antibiotic agents. For example, selectable markers may include genes for ampicillin resistance, streptomycin resistance, kanamycin resistance, tetracycline resistance, chloramphenicol resistance, sulfonamide resistance, or combinations of these markers. Typically, the selectable marker is operationally linked to a promoter that facilitates expression of the marker. Plasmids and other cloning vectors that include selectable markers are known in the art.

The DNA molecule typically is used to transform a host cell. Suitable host cells include any cell that is useful for storing and/or producing the DNA molecule.

Suitable host cells may include cells that expresses any gene present on the DNA molecule. Suitable host cells also may include cells that are capable of producing an organic acid in a fermentation process, such as succinic acid at a concentration suitable for commercial production (e.g., at least about 20 g/L, more suitably at least about 50 g/L, and more suitably at least about 100 g/L).

The methods for producing an organic acid typically include fermenting a nutrient medium with a recombinant microorganism that expresses a Zwf gene. For example, the method may include fermenting a nutrient medium with a recombinant A. succinogenes that expresses a Zwf gene (e.g., a heterologous Zwf gene such as the E. coli Zwf gene). Organic acids produced in the fermentation may include succinic acid. One suitable recombinant microorganism for the methods is a recombinant strain of A. succinogenes that expresses the E. coli Zwf gene, deposited under ATCC accession number PTA-6255. The methods also may include fermenting a nutrient medium with a recombinant strain of Bisgaard Taxon 6 or Bisgaard Taxon 10 that express a Zwf gene (e.g., a heterologous Zwf gene such as the E. coli Zwf gene) to produce succinic acid. The methods also may include fermenting a nutrient medium with a recombinant strain of E. coli that expresses a Zwf gene (or overexpresses a Zwf gene) to produce one or more organic acids such as lactic acid.

The methods may employ recombinant microorganisms that are resistant to relatively high levels of the organic acid being produced (e.g., succinic acid). The methods also may employ strains of microorganisms that are resistant to relatively high levels of undesirable by-products and/or strains of microorganisms that produce relatively low levels of undesirable by-products.

The nutrient medium typically includes a fermentable carbon source. The fermentable carbon source may be provided by a fermentable biomass. A fermentable biomass may be derived from a variety of crops and/or feedstocks including: sugar crops (e.g., sugar, beets, sweet sorghum, sugarcane, fodder beet); starch crops (e.g., grains such as corn, wheat, sorghum, barley, and tubers such as potatoes and sweet potatoes); cellulosic crops (e.g., corn stover, corn fiber, wheat straw, and forages such as Sudan grass forage, and sorghum). The biomass may be treated to facilitate release of fermentable carbon source (e.g., sugars). For example, the biomass may be treated with enzymes such as cellulase and/or xylanase, to release simple sugars. The fermentable carbon source may include simple sugars and sugar alcohols such as glucose, maltose, mannose, mannitol, sorbitol, galactose, xylose, arabinose, and mixtures thereof.

The methods typically result in a relatively high yield of succinic acid relative to an input carbon source such as glucose. For example, the methods may have a succinic acid yield (g) of at least about 90% relative to glucose input (g). Alternatively, the yield may be calculated as % succinic acid yield (mol)/glucose input (mol). As such, the methods may have a succinic acid yield (mol) of at least about 140% relative to glucose input (mol). Desirably, the methods may have a succinic acid yield (mol) of at least about 130% or at least about 170% relative to glucose input (mol).

The methods also typically result in a relatively high concentration of succinic acid production (e.g., relative to a method that uses a non-recombinant microorganism in a fermentation). For example, a fermentation may reach a concentration of at least about 50 g/L succinic acid. Desirably, a fermentation may reach a concentration of at least about 90 g/L succinic acid or more desirably, a concentration of at least about 130 g/L succinic acid. In some embodiments, the fermentation typically does not produce substantial levels of undesirable by-products such as acetate, formate, pyruvate, and mixtures thereof (e.g., no more than about 2.0 g/L acetate, no more than about 2.0 g/L formate, and/or no more than about 3.0 g/L pyruvate).

The methods may be used to produce relatively high concentration of lactic acid (e.g., relative to a method that uses a non-recombinant microorganism in a fermentation). For example, the recombinant microorganisms may be used in a fermentation to produce lactic acid at a concentration of at least about 25 g/L. In one embodiment, the fermentation yields may yield about 0.5 g lactic acid per gram glucose. The methods for producing lactic acid may include fermenting a suitable carbon source with recombinant E. coli that expresses (or overexpresses) a polypeptide that has one or more biochemical activities of the Zwf gene. For example, the method may include fermenting a suitable carbon source with recombinant E. coli that expresses the E. coli Zwf gene from an epigenetic element such as a plasmid.

Illustrated Embodiments

In one embodiment, the recombinant microorganism is a recombinant strain of Actinobacillus succinogenes that expresses a heterologous Zwf gene. The heterologous Zwf gene may be optimized for expression in Actinobacillus succinogenes. The heterologous Zwf gene may encode an E. coli Zwf enzyme. The recombinant strain may include recombinant Actinobacillus succinogenes deposited under ATCC Accession Number PTA-6255. The recombinant strain may be capable of producing succinic acid at concentrations of about 50 g/L to about 130 g/L (e.g., in a fermentation system that utilizes a suitable carbon source). The recombinant strain may be resistant to levels of sodium monofluoroacetate of at least about 1 g/L.

In some embodiments, the recombinant strain is a recombinant strain of microorganism belonging to Bisgaard Taxon 6 or Bisgaard Taxon 10 that expresses a heterologous Zwf gene. The heterologous Zwf gene may encode E. coli Zwf enzyme.

In another embodiment, the recombinant strain is a recombinant strain of Actinobacillus succinogenes, which includes a DNA molecule comprising a transcription promoter for Actinobacillus succinogenes operationally linked to a heterologous Zwf gene. The transcription promoter may include the A. succinogenes phosphoenolpyruvate (PEP) carboxykinase promoter or a variant thereof (e.g., a polynucleotide of SEQ ID NO:4 or a polynucleotide having at least about 95% sequence identity to SEQ ID NO:4, where the polynucleotide has A. succinogenes phosphoenolpyruvate (PEP) carboxykinase promoter activity). The heterologous Zwf gene may encode E. coli Zwischenferment enzyme or a variant thereof (e.g., a polynucleotide of SEQ ID NO:1 or a polynucleotide having at least about 95% sequence identity to SEQ ID NO:1, where the polynucleotide has E. coli Zwischenferment enzyme activity). The heterologous Zwf gene may include the E. coli Zwf gene. Optionally, the Zwf gene may be optimized for expression in Actinobacillus succinogenes. The DNA molecule may be epigenetic (e.g., present on a plasmid). The DNA molecule may include a selectable marker (e.g., kanamycin resistance, ampicillin resistance, streptomycin resistance, sulfonamide resistance, tetracycline resistance, chloramphenicol resistance, or a combination thereof).

In another embodiment, the recombinant strain is a recombinant strain of Actinobacillus succinogenes which comprises a heterologous Zwf enzyme. The heterologous Zwf enzyme may be expressed from a Zwf gene that has been optimized for expression in Actinobacillus succinogenes. The heterologous Zwf enzyme may include E. coli Zwischenferment enzyme. The recombinant strain may include recombinant A. succinogenes deposited under ATCC Accession Number PTA-6255. The recombinant strain may be capable of producing succinic acid at concentrations of about 50 g/L to about 130 g/L. Optionally, the recombinant strain is resistant to levels of sodium monofluoroacetate of at least about 1 g/L.

In one embodiment, the method for producing succinic acid includes fermenting a nutrient medium with a recombinant microorganism that expresses a heterologous Zwf gene. The recombinant microorganism may include a recombinant strain of Actinobacillus succinogenes (e.g., A. succinogenes recombinant strain deposited under ATCC Accession Number PTA-6255). The recombinant microorganism may include a recombinant strain of Bisgaard Taxon 6 or a recombinant strain of Bisgaard Taxon 10. The heterologous Zwf gene may include the E. coli Zwf gene. Optionally, the recombinant strain is resistant to levels of sodium monofluoroacetate of at least about 1 g/L. Optionally, the recombinant strain is capable of producing succinic acid at concentrations of about 50 g/L to about 130 g/L. The nutrient medium may include a fermentable sugar (e.g., glucose). Typically, the method results in a succinic acid yield (g) of at least about 100% relative to glucose (g).

In one embodiment, the recombinant DNA molecule includes a transcription promoter for A. succinogenes operationally linked to a heterologous Zwf gene. For example, the transcription promoter may include the A. succinogenes phosphoenolpyruvate (PEP) carboxykinase promoter or a variant thereof, (e.g., a polynucleotide of SEQ ID NO:4 or a polynucleotide having at least about 95% sequence identity to SEQ ID NO:4, where the polynucleotide has Actinobacillus succinogenes phosphoenolpyruvate (PEP) carboxykinase promoter activity).

In one embodiment, the recombinant DNA molecule is present in a DNA plasmid. Typically, the DNA plasmid includes a selectable marker (e.g., a gene selected from the group consisting of ampicillin resistance, kanamycin resistance, streptomycin resistance, tetracycline resistance, chloramphenicol resistance, sulfonamide resistance, and combinations thereof). The DNA molecule, which may be present in a DNA plasmid, may be present in a host cell. The host cell may be capable of producing succinic acid at concentrations of about 50 g/L to about 130 g/L in a fermentation system.

In one embodiment, the recombinant microorganism is a recombinant strain of a succinic acid producing microorganism which has been transformed with a DNA molecule that expresses a polypeptide having Zwf enzyme activity. The DNA molecule may include a polynucleotide that encodes a polypeptide having Zwf enzyme activity, which may include NADP reductase activity. The DNA molecule may include a polynucleotide that encodes a polypeptide having at least about 90% sequence identity (or desirably at least about 95% sequence identity) to the amino acid sequence of a Zwf enzyme (e.g., SEQ ID NO:3 or SEQ ID NO:6), where the polypeptide has Zwf enzyme activity (e.g., NADP reductase activity). The DNA molecule may include a polynucleotide sequence having at least about 90% sequence identity (or desirably at least about 95% sequence identity) to the polynucleotide sequence of a Zwf gene (e.g., SEQ ID NO:1; SEQ ID NO:2; or SEQ ID NO:5), where the polynucleotide encodes a polypeptide having Zwf enzyme activity. In some embodiments, the recombinant strain may be derived from a microorganism whose 16S rRNA has at least about 90% sequence identity to 16S rRNA of Actinobacillus succinogenes. For example, the recombinant strain may be derived from a strain of Actinobacillus succinogenes, Bisgaard Taxon 6, or Bisgaard Taxon 10.

In another embodiment, the recombinant microorganism is a recombinant strain of a succinic acid producing microorganism that has been transformed with a heterologous Zwf gene. The heterologous Zwf gene may be optimized for expression in the microorganism. In some embodiments, the heterologous Zwf gene may encode E. coli Zwf enzyme. In some embodiments, the Zwf gene may include a polynucleotide having at least about 95% sequence identity to SEQ ID NO:1, where the polynucleotide has Zwf enzyme activity.

In another embodiment, the recombinant microorganism is a recombinant strain of a succinic acid producing microorganism that has been transformed with a DNA molecule that includes a transcription promoter for phosphoenolpyruvate (PEP) carboxykinase operationally linked to polynucleotide encoding a polypeptide having Zwf enzyme activity. The transcription promoter may include the Actinobacillus succinogenes phosphoenolpyruvate (PEP) carboxykinase promoter. In some embodiments, the promoter may include a polynucleotide having at least about 95% sequence identity to SEQ ID NO:4, where the polynucleotide has promoter activity.

In another embodiment, the recombinant microorganism is a recombinant strain transformed with a DNA molecule that is epigenetic. The DNA molecule may be present on a plasmid.

In another embodiment, the recombinant microorganism is a recombinant strain that is capable of producing succinic acid at concentrations of about 50 g/L to about 130 g/L.

The recombinant strain may be resistant to levels of sodium monofluoroacetate of at least about 1 g/L. In some embodiments, the recombinant strain is recombinant Actinobacillus succinogenes deposited under ATCC Accession Number PTA-6255.

In another embodiment, the recombinant microorganism is used for producing succinic acid in a method that include fermenting a nutrient medium with the recombinant microorganism. The nutrient medium typically includes fermentable sugar such as glucose. The method may result in a succinic acid yield (g) of at least about 100% relative to glucose (g).

In some embodiments, the DNA molecule comprising a transcription promoter for a succinic acid producing microorganism operationally linked to a heterologous Zwf gene. The transcription promoter may include a phosphoenolpyruvate (PEP) carboxykinase promoter. In some embodiments, the promoter includes a polynucleotide having at least about 95% sequence identity to SEQ ID NO:4, where the polynucleotide has promoter activity. The DNA molecule may be present within a plasmid. The DNA molecule may be present in a host cell (e.g., a host cell capable of producing succinic acid at concentrations of about 50 g/L to about 130 g/L).

EXAMPLES
Microorganism Strains and Plasmids

A. succinogenes strain FZ45 is a stable bacterial variant of Actinobacillus succinogenes 130Z, which is resistant to sodium monofluoroacetate. See Guettler et al., INT'L J. SYST. BACT. (1999) 49:207-216; and U.S. Pat. No. 5,573,931. The E. coli-A. succinogenes shuttle vector pLS88 (deposited at the American Type Culture Collection as ATCC accession no. 86980) was obtained from Dr. Leslie Slaney, University of Manitoba, Canada. Plasmid pLS88 is described as having been isolated from Haenzophilus ducreyi and may confer resistance to sulfonamides, streptomycin, and kanamycin.

Genetic Manipulations

Recombinant DNA manipulations generally followed methods described in the art. Plasmid DNA was prepared by the alkaline lysis method. Typical resuspension volumes for multicopy plasmids extracted from 1.5 ml cultures were 50 μl. Larger DNA preparation used the Qiagen Plasmid Purification Midi and Maxi kit according to the manufacturer's instructions. Restriction endonucleases, Molecular Weight Standards, and pre-stained markers were purchased from New England Biolabs and Invitrogen and digests were performed as recommended by the manufacturers, except that an approximately 5-fold excess of enzyme was used. DNA was analyzed on Tris-acetate-agarose gels in the presence of ethidium bromide. DNA was extracted from agarose gels and purified using the Qiagen gel extraction kit according to the manufacturer's instructions. DNA was dephosphorylated using shrimp alkaline phosphatase (Roche) in combination with restriction digests. The phosphatase was heat inactivated at 70° C. for 15 min. Ligations were performed using a 3- to 5-fold molar excess of insert to vector DNA in a 20 μl reaction volume and 1 μl of T4 DNA Ligase (New England Biolabs) for 1 hour at 25° C. E. coli transformation were performed by using “library efficiency competent cells” purchased from Invitrogen, following the manufacturer's instructions.

Transformations using ligation mixes were plated without dilutions on standard LB plates containing the appropriate antibiotic. PCR amplifications were carried out using the Perkin Elmer manual as a guideline. Primer designs were based on published sequences (as provided a the National Center for Biotechnology Information (NCBI) database). The primers included engineered restriction enzyme recognition sites. Primers were analyzed for dimer and hairpin formation and melting temperature using the Vector NTI program. All primers were ordered from the Michigan State Macromolecular Structure Facility. PCR amplifications were carried out in an Eppendorf Gradient Master Cycler, or in a Perkin Elmer Thermocycler. Starting annealing temperatures were determined using the Vector NTI program for each primer pair. Restriction enzymes for digesting the amplified products were purchased from Invitrogen or New England Biolabs.

The Zwf gene from E. coli was amplified from strain BL21(DE3) genomic DNA (ATCC accession number NC—000913), using the following primers: Forward, 5′-CCGCTCGAGGGCGGTAACGCAAACAGC (SEQ ID NO:9); and Reverse, 5′-CCGCTCGAGTTACTCAAACTCATTCCAGG (SEQ ID NO:10). XhoI restriction sequences (underlined nucleotides) were included to facilitate cloning and the ensuing 1.5 kb Zwf fragment was inserted into the SalI site of pJR762.55 to produce plasmid pJR762.73.

Transformation of A. succinogenes

A. succinogenes competent cells for electroporation were prepared by growing cells in tryptic soy broth medium (TSB) to an OD600 of ˜0.6. Cells were spun down, washed twice with sterile water, twice with 10% v/v glycerol and resuspended in 0.01× the original culture volume with 10% glycerol. Cells were flash frozen and stored at minus 80° C. Approximately 40 μl of thawed cells were used for electroporation, in 0.1 cm cuvettes with a BioRad GenePulser at settings of 400 W, 25 mF, and 1.8 kV. Following electroporation, 1 ml room temperature TSB medium was immediately added and the cells were incubated at 37° C. for 1 h. The cell solution was plated on TSB agar plates containing Kanamycin (100 μg/ml).

Optical density determination of A. succinogenes

Samples from magnesium-neutralized fermentations were spun at 420×g for 2 min to precipitate the MgCO3 and diluted with 0.5N HCl to solubilize any remaining precipitate before reading at OD660.

For fermentations that required a measure of growth through optical density measurements a cold water extract of LFS was used. Suspended solids and some oils were removed through centrifugation of LFS in a Sorvall GSA rotor, at 9,000 rpm for 20 minutes. The supernatant was allowed to settle in a separation funnel for 3 hours at room temperature. The lower water phase typically represented 57% (w/v) of the raw LFS.

E. coli strains DH5α/pJR762.73 (Zwf), DH5α/pJR762.17 (Zwf), and DH5α/pLS88 were grown in NBS 5-liter Bioflo III fermentors using four liters of the following medium: 900AG yeast extract 15 g; corn steep liquor 15 g; Na2HPO4 1.16 g; NaH2PO4.H20, 0.84 g: (NH4)2SO4 3 g; MgSO4.7H2O, 0.61; CaCl2.2H2O, 0.25 g, and glucose, 45 g per liter. The pH was controlled at 6.7 through the automatic addition of K2CO3 (3.3N). The fermentations were each started with a 1.25% inoculum. Conditions were initially made aerobic which favored the rapid growth of the E. coli cells; stirring was at 500 rpm and the medium was sparged with air at 0.5 liter/liter-min. Fermentor conditions were made anaerobic to favor organic acid production when the cell density reached a minimum of 6.2 OD660 units; then the medium was sparged with 0.2 liter/liter-min of a CO2 and H2 mixture (95:5), and stirring was reduced to 250 rpm. Samples were taken periodically and the organic acid products and residual glucose concentrations were determined through HPLC.

Analysis of Fermentation Broths

Succinic acid, glucose, lactic acid, pyruvate, ethanol, and formic acid concentrations were determined by reverse phase high pressure liquid chromatography (HPLC) using a Waters 1515 Isocratic pump with a Waters 717 Auto sampler and a Waters 2414 refractive index detector set at 35° C. The HPLC system was controlled, data collected and processed using Waters Breeze software (version 3.3). A Bio-Rad Aminex HPX-87H (300 mm×7.8 mm) column was used with a cation H guard column held at 55° C. The mobile phase was 0.021 N sulfuric acid running at 0.5 ml/min. Samples were filter through a 0.45 μm filter, and 5.0 μl was injected onto the column. Run time was thirty minutes.

CO2 Measurements

A mass flow controller (Brooks model 58501) was used to monitor and supply CO2 to the fermentor sparging system at 100 ml/min. A mass flow meter (Brooks model 5860I) was used to measure CO2 exiting the fermentor by way of the exhaust condenser system. The two CO2 flow meters were connected to a computer via a 4-20 ma Bio-Command Interface. The BioCommand Plus Bioprocessing software logged the inlet and outlet CO2 flow every 60 seconds. The rate of CO2 consumption (ml/min) was expressed as the difference between the inlet and outlet rates during any given minute (CO2use=CO2in−CO2out). The volume of CO2 consumed during any given fermentation interval is the sum of rates each minute of the interval. The moles of CO2 consumed were calculated using the Ideal Gas Law, (consumed liters÷22.4 liters/mole=consumed moles).

The mass flow meters were calibrated by the manufacturer for CO2 and their precision was 1% of full scale or 2 ml/m. The fermentation set-up was monitored for gas leaks by mixing 5% hydrogen into the CO2. Hydrogen leaks were detected using a Tif8800 CO/Combustible Gas analyzer.

Metabolic Flux Analysis of A. Succinogenes Fermentations

The metabolic flux distributions (MFA) during anaerobic succinic acid production in Actinobacillus succinogenes were analyzed using the FluxAnalyzer software package. The FluxAnalyzer package was obtained from Professor Steffen Klamt (Max Planck Institute, Magdeburg, Germany) and was operated according to the instructions provided in the manual. The FluxAnalyzer package facilitates the analysis of metabolic fluxes by providing a graphical user interface for the MATLAB program, which performs the actual mathematical calculations. The MATLAB software was purchased from MathWork Inc. By measuring the changes in extracellular concentrations of the known and expected components of the entire metabolic pathway, the intracellular fluxes for the major intracellular metabolites were calculated using the metabolic network model described below. The specific network (labeled A—succinogenes) was constructed using the 20 known metabolites and 27 reactions shown below (without considerations of biomass composition and growth rate):

Fermentation samples were analyzed over the time course of the fermentations using the analytical methods previously described. Concentrations of glucose, glycerol, arabinose, xylose, sorbitol, succinic acid, acetic acid, ethanol, pyruvate, lactic acid and fermentation volumes were determined at each sampling time. The amount of metabolite was calculated according to the formula: (metabolite, g)=V (fermentor, 1)*C(metabolite, g/l). The metabolite consumption rate or the metabolite production rate during the time period of t0−t1 was calculated using the formula: Metabolite consumption rate (mol/h, t0and t1)=[Amount (metabolite, g, t0)−Amount (metabolite, g, t1)]/[(t1−t0)*Molecular Weight of Metabolite]. For comparison of metabolic flux for all the time periods, the consumption rate or production rate of metabolite in the flux map was adjusted, assuming a glucose consumption rate in the flux map of 100. The metabolite consumption or production rate in the map “Mcp” was determined according to the following formula: Mcp=(metabolic consumption/or production rate)×100/(glucose consumption rate).

The consumption or production rates of the various metabolites were input into the metabolic network model in the FluxAnalyzer package according to the operating instructions. The function “Calculate/Balance Rates” was used to calculate all the calculatable rates. If the system was non-redundant, an optimization procedure was started, where a linear objective function was minimized. If the system was redundant, one or more of three methods (simple least squares, variances-weighted least squares I and variances weighted least squares II) were applied to calculate the rates. The flux rate was shown directly on the flux map. Final flux map were copied into Microsoft Excel files for storage purposes.

Metabolic flux analysis was used to evaluate the effect of different carbon sources on succinic acid production in batch fermentations with A. succinogenes FZ45. The analyses established that the major pathway for succinic acid production in A. succinogenes FZ45 flows in the following manner: phosphoenolpyruvate (PEP)→oxaloacetate (OAA)→malate→fumarate→succinic acid. The glyoxylate shunt and the PEP-transport-system (PTS) appear not to be substantially used in the organism. Glucose fermentations reach a concentration of 61.7 g/L succinic acid with a yield of about 94% (succinic acid (g)/glucose (g)). Fermentations performed using a more reduced carbon source, such as sorbitol, produced higher amounts of succinic acid (77.3 g/L) with a higher yield (108% succinic acid (g)/glucose (g)), indicating that reducing power may become a limiting factor during the fermentation of glucose.

Enhanced Succinic Acid Production from Glucose by Over-Expression of Zwf

Strains FZ45, FZ45/pLS88 and FZ45/pJR762.73 were cultured under standard production conditions with the exception that 100 μg/ml kanamycin was added to the fermentation medium for the transformed strains. FZ45/pLS88 served as a second control, and is transformed with the cloning vector, carrying no PEP carboxykinase promoter or Zwf gene. The carbon source used was glucose. The strain FZ45/pJR762.73 showed an increase in succinic acid production over the control strains FZ45 and FZ45/pLS88, with a corresponding increase in the final concentration of succinic acid. The total amount of succinic acid produced from glucose increased from 284 g to 302 g, the molar yield of succinic acid produced increased from 144% to 155% (moles succinic acid/100 moles glucose), the weight yield increased from 94.7% to 101.9%, and the final concentration of succinic acid in the fermentation broth increased from 62 g/L to 65 g/L. These results are summarized in Table 1. All transformed FZ45 derivatives exhibit slower growth compared to the untransformed FZ45, which may be caused by the replication of the additional extrachromosomal plasmid DNA.

Metabolic flux analyses on both FZ45 and FZ45/pJR762.73 showed that FZ45/pJR762.73 channeled more carbon into the pentose phosphate pathway than the untransformed FZ45 (see FIG. 1 and FIG. 2). Thus, over-expression of the Zwf protein was sufficient to enhance succinic acid yields and to reduce the production of other metabolites when glucose was used as carbon source.

Fermentation with A. Succinogenes FZ45/pJR762.73 Using a Reduced Carbon Source

Fermentations with A. succinogenes FZ45/pJR762.73 utilizing mannitol as a carbon source were also performed. Mannitol is a 6-carbon sugar-alcohol that is more reduced than glucose. Expression of Zwf also enhanced succinic acid production using mannitol (see Table 3). However, fermentations using this sugar alcohol also showed increased yields even with the untransformed strain FZ45. This indicates that increasing the amount of metabolic reducing equivalents will enhance succinic acid production.

The effect of Zwf expression in other species was also tested using the organisms Bisgaard Taxon 6 (BT6) and Bisgaard Taxon 10 (BT10). Both organisms belong to the family Pasteurellaceae, and are related to A. succinogenes. Also, both organisms are known to produce succinic acid. Using the methods described above and the same plasmid, pJR762.73 (carrying the Zwf gene under the A. succinogenes PEPCK promoter), Bisgaard Taxa were transformed. Both these transformed strains showed an increase in succinic acid production using glucose as the carbon source. These results are shown in Table 4 below.

Flux analysis of these fermentations with the Bisgaard Taxa strains indicated that use of the pentose phosphate pathway was indeed increased in the strains carrying the plasmid. BT6/pJR762.73 routed more carbon through the pentose phosphate pathway than the control (33 mol % vs. 20 mol %). Similarly, BT10/pJR762.73 routed 35 mol % carbon through the pentose phosphate pathway, compared to only 5 mol % in the control.

It will be readily apparent to one skilled in the art that varying substitutions and modifications may be made to the invention disclosed herein without departing from the scope and spirit of the invention. The invention illustratively described herein suitably may be practiced in the absence of any element or elements, limitation or limitations which is not specifically disclosed herein. The terms and expressions which have been employed are used as terms of description and not of limitation, and there is no intention that in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention. Thus, it should be understood that although the present invention has been illustrated by specific embodiments and optional features, modification and/or variation of the concepts herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention.

In addition, where features or aspects of the invention are described in terms of Markush groups or other grouping of alternatives, those skilled in the art will recognize that the invention is also thereby described in terms of any individual member or subgroup of members of the Markush group or other group.

Also, unless indicated to the contrary, where various numerical values are provided for embodiments, additional embodiments are described by taking any 2 different values as the endpoints of a range. Such ranges are also within the scope of the described invention.

All references, patents, and/or applications cited in the specification are incorporated by reference in their entireties, including any tables and figures, to the same extent as if each reference had been incorporated by reference in its entirety individually.

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